251
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Structural insight into substrate preference for TET-mediated oxidation. Nature 2015; 527:118-22. [PMID: 26524525 DOI: 10.1038/nature15713] [Citation(s) in RCA: 191] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 09/10/2015] [Indexed: 12/19/2022]
Abstract
DNA methylation is an important epigenetic modification. Ten-eleven translocation (TET) proteins are involved in DNA demethylation through iteratively oxidizing 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Here we show that human TET1 and TET2 are more active on 5mC-DNA than 5hmC/5fC-DNA substrates. We determine the crystal structures of TET2-5hmC-DNA and TET2-5fC-DNA complexes at 1.80 Å and 1.97 Å resolution, respectively. The cytosine portion of 5hmC/5fC is specifically recognized by TET2 in a manner similar to that of 5mC in the TET2-5mC-DNA structure, and the pyrimidine base of 5mC/5hmC/5fC adopts an almost identical conformation within the catalytic cavity. However, the hydroxyl group of 5hmC and carbonyl group of 5fC face towards the opposite direction because the hydroxymethyl group of 5hmC and formyl group of 5fC adopt restrained conformations through forming hydrogen bonds with the 1-carboxylate of NOG and N4 exocyclic nitrogen of cytosine, respectively. Biochemical analyses indicate that the substrate preference of TET2 results from the different efficiencies of hydrogen abstraction in TET2-mediated oxidation. The restrained conformation of 5hmC and 5fC within the catalytic cavity may prevent their abstractable hydrogen(s) adopting a favourable orientation for hydrogen abstraction and thus result in low catalytic efficiency. Our studies demonstrate that the substrate preference of TET2 results from the intrinsic value of its substrates at their 5mC derivative groups and suggest that 5hmC is relatively stable and less prone to further oxidation by TET proteins. Therefore, TET proteins are evolutionarily tuned to be less reactive towards 5hmC and facilitate the generation of 5hmC as a potentially stable mark for regulatory functions.
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252
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Liu S, Jiang J, Li L, Amato NJ, Wang Z, Wang Y. Arsenite Targets the Zinc Finger Domains of Tet Proteins and Inhibits Tet-Mediated Oxidation of 5-Methylcytosine. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:11923-31. [PMID: 26355596 PMCID: PMC4784102 DOI: 10.1021/acs.est.5b03386] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Arsenic toxicity is a serious public health problem worldwide that brings more than 100 million people into the risk of arsenic exposure from groundwater and food contamination. Although there is accumulating evidence linking arsenic exposure with aberrant cytosine methylation in the global genome or at specific genomic loci, very few have investigated the impact of arsenic on the oxidation of 5-methylcytosine (5-mC) mediated by the Ten-eleven translocation (Tet) family of proteins. Owing to the high binding affinity of As(III) toward cysteine residues, we reasoned that the highly conserved C3H-type zinc fingers situated in Tet proteins may constitute potential targets for arsenic binding. Herein, we found that arsenite could bind directly to the zinc fingers of Tet proteins in vitro and in cells, and this interaction substantially impaired the catalytic efficiency of Tet proteins in oxidizing 5-mC to 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-foC), and 5-carboxylcytosine (5-caC). Treatments with arsenite also led to a dose-dependent decrease in the level of 5-hmC, but not 5-mC, in DNA isolated from HEK293T cells overexpressing the catalytic domain of any of the three Tet proteins and from mouse embryonic stem cells. Together, our study unveiled, for the first time, that arsenite could alter epigenetic signaling by targeting the zinc fingers of Tet proteins and perturbing the Tet-mediated oxidation of 5-mC in vitro and in cells. Our results offer important mechanistic understanding of arsenic epigenotoxicity and carcinogenesis in mammalian systems and may lead to novel approaches for the chemoprevention of arsenic toxicity.
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Affiliation(s)
- Shuo Liu
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
| | - Ji Jiang
- Cell, Molecular and Developmental Biology Graduate Program, University of California, Riverside, California 92521, United States
| | - Lin Li
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Nicholas J. Amato
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
| | - Zi Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
- Cell, Molecular and Developmental Biology Graduate Program, University of California, Riverside, California 92521, United States
- Department of Chemistry, University of California, Riverside, California 92521, United States
- Corresponding Author. Phone: 951-827-2700; fax: 951-827-4713;
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253
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Salminen A, Kauppinen A, Kaarniranta K. 2-Oxoglutarate-dependent dioxygenases are sensors of energy metabolism, oxygen availability, and iron homeostasis: potential role in the regulation of aging process. Cell Mol Life Sci 2015; 72:3897-914. [PMID: 26118662 PMCID: PMC11114064 DOI: 10.1007/s00018-015-1978-z] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/10/2015] [Accepted: 06/22/2015] [Indexed: 02/06/2023]
Abstract
Recent studies have revealed that the members of an ancient family of nonheme Fe(2+)/2-oxoglutarate-dependent dioxygenases (2-OGDO) are involved in the functions associated with the aging process. 2-Oxoglutarate and O2 are the obligatory substrates and Fe(2+) a cofactor in the activation of 2-OGDO enzymes, which can induce the hydroxylation of distinct proteins and the demethylation of DNA and histones. For instance, ten-eleven translocation 1-3 (TET1-3) are the demethylases of DNA, whereas Jumonji C domain-containing histone lysine demethylases (KDM2-7) are the major epigenetic regulators of chromatin landscape, known to be altered with aging. The functions of hypoxia-inducible factor (HIF) prolyl hydroxylases (PHD1-3) as well as those of collagen hydroxylases are associated with age-related degeneration. Moreover, the ribosomal hydroxylase OGFOD1 controls mRNA translation, which is known to decline with aging. 2-OGDO enzymes are the sensors of energy metabolism, since the Krebs cycle intermediate 2-oxoglutarate is an activator whereas succinate and fumarate are the potent inhibitors of 2-OGDO enzymes. In addition, O2 availability and iron redox homeostasis control the activities of 2-OGDO enzymes in tissues. We will briefly elucidate the catalytic mechanisms of 2-OGDO enzymes and then review the potential functions of the above-mentioned 2-OGDO enzymes in the control of the aging process.
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Affiliation(s)
- Antero Salminen
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland.
| | - Anu Kauppinen
- Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland
- Department of Ophthalmology, Kuopio University Hospital, P.O.B. 100, 70029, Kuopio, Finland
| | - Kai Kaarniranta
- Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland.
- Department of Ophthalmology, Kuopio University Hospital, P.O.B. 100, 70029, Kuopio, Finland.
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254
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Li W, Zhang T, Ding J. Molecular basis for the substrate specificity and catalytic mechanism of thymine-7-hydroxylase in fungi. Nucleic Acids Res 2015; 43:10026-38. [PMID: 26429971 PMCID: PMC4787775 DOI: 10.1093/nar/gkv979] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/18/2015] [Indexed: 12/17/2022] Open
Abstract
TET proteins play a vital role in active DNA demethylation in mammals and thus have important functions in many essential cellular processes. The chemistry for the conversion of 5mC to 5hmC, 5fC and 5caC catalysed by TET proteins is similar to that of T to 5hmU, 5fU and 5caU catalysed by thymine-7-hydroxylase (T7H) in the nucleotide anabolism in fungi. Here, we report the crystal structures and biochemical properties of Neurospora crassa T7H. T7H can bind the substrates only in the presence of cosubstrate, and binding of different substrates does not induce notable conformational changes. T7H exhibits comparable binding affinity for T and 5hmU, but 3-fold lower affinity for 5fU. Residues Phe292, Tyr217 and Arg190 play critical roles in substrate binding and catalysis, and the interactions of the C5 modification group of substrates with the cosubstrate and enzyme contribute to the slightly varied binding affinity and activity towards different substrates. After the catalysis, the products are released and new cosubstrate and substrate are reloaded to conduct the next oxidation reaction. Our data reveal the molecular basis for substrate specificity and catalytic mechanism of T7H and provide new insights into the molecular mechanism of substrate recognition and catalysis of TET proteins.
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Affiliation(s)
- Wenjing Li
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Tianlong Zhang
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Jianping Ding
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China Collaborative Innovation Center for Genetics and Development, Fudan University, 2005 Song-Hu Road, Shanghai 200438, China
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255
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TET2 repression by androgen hormone regulates global hydroxymethylation status and prostate cancer progression. Nat Commun 2015; 6:8219. [PMID: 26404510 DOI: 10.1038/ncomms9219] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 07/30/2015] [Indexed: 12/13/2022] Open
Abstract
Modulation of epigenetic patterns has promising efficacy for treating cancer. 5-Hydroxymethylated cytosine (5-hmC) is an epigenetic mark potentially important in cancer. Here we report that 5-hmC is an epigenetic hallmark of prostate cancer (PCa) progression. A member of the ten-eleven translocation (TET) proteins, which catalyse the oxidation of methylated cytosine (5-mC) to 5-hmC, TET2, is repressed by androgens in PCa. Androgen receptor (AR)-mediated induction of the miR-29 family, which targets TET2, are markedly enhanced in hormone refractory PCa (HRPC) and its high expression predicts poor outcome of PCa patients. Furthermore, decreased expression of miR-29b results in reduced tumour growth and increased TET2 expression in an animal model of HRPC. Interestingly, global 5-hmC modification regulated by miR-29b represses FOXA1 activity. A reduction in 5-hmC activates PCa-related key pathways such as mTOR and AR. Thus, DNA modification directly links the TET2-dependent epigenetic pathway regulated by AR to 5-hmC-mediated tumour progression.
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256
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Hashimoto H, Pais JE, Dai N, Corrêa IR, Zhang X, Zheng Y, Cheng X. Structure of Naegleria Tet-like dioxygenase (NgTet1) in complexes with a reaction intermediate 5-hydroxymethylcytosine DNA. Nucleic Acids Res 2015; 43:10713-21. [PMID: 26323320 PMCID: PMC4678852 DOI: 10.1093/nar/gkv870] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 08/19/2015] [Indexed: 01/15/2023] Open
Abstract
The family of ten-eleven translocation (Tet) dioxygenases is widely distributed across the eukaryotic tree of life, from mammals to the amoeboflagellate Naegleria gruberi. Like mammalian Tet proteins, the Naegleria Tet-like protein, NgTet1, acts on 5-methylcytosine (5mC) and generates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) in three consecutive, Fe(II)- and α-ketoglutarate-dependent oxidation reactions. The two intermediates, 5hmC and 5fC, could be considered either as the reaction product of the previous enzymatic cycle or the substrate for the next cycle. Here we present a new crystal structure of NgTet1 in complex with DNA containing a 5hmC. Along with the previously solved NgTet1–5mC structure, the two complexes offer a detailed picture of the active site at individual stages of the reaction cycle. In the crystal, the hydroxymethyl (OH-CH2-) moiety of 5hmC points to the metal center, representing the reaction product of 5mC hydroxylation. The hydroxyl oxygen atom could be rotated away from the metal center, to a hydrophobic pocket formed by Ala212, Val293 and Phe295. Such rotation turns the hydroxyl oxygen atom away from the product conformation, and exposes the target CH2 towards the metal-ligand water molecule, where a dioxygen O2 molecule would occupy to initiate the next round of reaction by abstracting a hydrogen atom from the substrate. The Ala212-to-Val (A212V) mutant profoundly limits the product to 5hmC, probably because the reduced hydrophobic pocket size restricts the binding of 5hmC as a substrate.
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Affiliation(s)
- Hideharu Hashimoto
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
| | - June E Pais
- New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Nan Dai
- New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Ivan R Corrêa
- New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Xing Zhang
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
| | - Yu Zheng
- RGENE Inc., 953 Indiana Street, San Francisco, CA, 94107, USA
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
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257
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Li D, Guo B, Wu H, Tan L, Lu Q. TET Family of Dioxygenases: Crucial Roles and Underlying Mechanisms. Cytogenet Genome Res 2015; 146:171-80. [PMID: 26302812 DOI: 10.1159/000438853] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Indexed: 11/19/2022] Open
Abstract
DNA methylation plays an important role in the epigenetic regulation of mammalian gene expression. TET (ten-eleven translocation) proteins, newly discovered demethylases, have sparked great interest since their discovery. TET proteins catalyze 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine in 3 consecutive Fe(II)- and 2-oxoglutarate (2-OG)-dependent oxidation reactions. TET proteins dynamically regulate global or locus-specific 5-methylcytosine and/or 5-hydroxymethylcytosine levels by facilitating active DNA demethylation. In fact, in addition to their role as methylcytosine dioxygenases, TET proteins are closely related to histone modification, interact with metabolic enzymes as well as other proteins, and cooperate in transcriptional regulation. In this review, we summarize the recent progress in this exciting field, highlighting the molecular mechanism by which TET enzymes regulate gene expression and their functions in health and disease. We also discuss the therapeutic potential of targeting TET proteins and aberrant DNA modifications.
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Affiliation(s)
- Duo Li
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, China
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258
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Ko M, An J, Pastor WA, Koralov SB, Rajewsky K, Rao A. TET proteins and 5-methylcytosine oxidation in hematological cancers. Immunol Rev 2015; 263:6-21. [PMID: 25510268 DOI: 10.1111/imr.12239] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA methylation has pivotal regulatory roles in mammalian development, retrotransposon silencing, genomic imprinting, and X-chromosome inactivation. Cancer cells display highly dysregulated DNA methylation profiles characterized by global hypomethylation in conjunction with hypermethylation of promoter CpG islands that presumably lead to genome instability and aberrant expression of tumor suppressor genes or oncogenes. The recent discovery of ten-eleven-translocation (TET) family dioxygenases that oxidize 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) in DNA has led to profound progress in understanding the mechanism underlying DNA demethylation. Among the three TET genes, TET2 recurrently undergoes inactivating mutations in a wide range of myeloid and lymphoid malignancies. TET2 functions as a bona fide tumor suppressor particularly in the pathogenesis of myeloid malignancies resembling chronic myelomonocytic leukemia (CMML) and myelodysplastic syndromes (MDS) in human. Here we review diverse functions of TET proteins and the novel epigenetic marks that they generate in DNA methylation/demethylation dynamics and normal and malignant hematopoietic differentiation. The impact of TET2 inactivation in hematopoiesis and various mechanisms modulating the expression or activity of TET proteins are also discussed. Furthermore, we also present evidence that TET2 and TET3 collaborate to suppress aberrant hematopoiesis and hematopoietic transformation. A detailed understanding of the normal and pathological functions of TET proteins may provide new avenues to develop novel epigenetic therapies for treating hematological malignancies.
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Affiliation(s)
- Myunggon Ko
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
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259
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Li C, Lan Y, Schwartz-Orbach L, Korol E, Tahiliani M, Evans T, Goll MG. Overlapping Requirements for Tet2 and Tet3 in Normal Development and Hematopoietic Stem Cell Emergence. Cell Rep 2015; 12:1133-43. [PMID: 26257178 DOI: 10.1016/j.celrep.2015.07.025] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 06/19/2015] [Accepted: 07/10/2015] [Indexed: 11/29/2022] Open
Abstract
The Tet family of methylcytosine dioxygenases (Tet1, Tet2, and Tet3) convert 5-methylcytosine to 5-hydroxymethylcytosine. To date, functional overlap among Tet family members has not been examined systematically in the context of embryonic development. To clarify the potential for overlap among Tet enzymes during development, we mutated the zebrafish orthologs of Tet1, Tet2, and Tet3 and examined single-, double-, and triple-mutant genotypes. Here, we identify Tet2 and Tet3 as the major 5-methylcytosine dioxygenases in the zebrafish embryo and uncover a combined requirement for Tet2 and Tet3 in hematopoietic stem cell (HSC) emergence. We demonstrate that Notch signaling in the hemogenic endothelium is regulated by Tet2/3 prior to HSC emergence and show that restoring expression of the downstream gata2b/scl/runx1 transcriptional network can rescue HSCs in tet2/3 double mutant larvae. Our results reveal essential, overlapping functions for tet genes during embryonic development and uncover a requirement for 5hmC in regulating HSC production.
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Affiliation(s)
- Cheng Li
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Program in Biochemistry and Structural Biology, Cell and Developmental Biology, and Molecular Biology, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Yahui Lan
- Department of Surgery, Weill Cornell Medical College, New York, NY 10065, USA
| | - Lianna Schwartz-Orbach
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Evgenia Korol
- Department of Biochemistry and Molecular Pharmacology, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Mamta Tahiliani
- Department of Biochemistry and Molecular Pharmacology, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Todd Evans
- Department of Surgery, Weill Cornell Medical College, New York, NY 10065, USA
| | - Mary G Goll
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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260
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Qiao Y, Wang X, Wang R, Li Y, Yu F, Yang X, Song L, Xu G, Chin YE, Jing N. AF9 promotes hESC neural differentiation through recruiting TET2 to neurodevelopmental gene loci for methylcytosine hydroxylation. Cell Discov 2015; 1:15017. [PMID: 27462416 PMCID: PMC4860857 DOI: 10.1038/celldisc.2015.17] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 05/25/2015] [Indexed: 01/23/2023] Open
Abstract
AF9 mutations have been implicated in human neurodevelopmental diseases and murine Af9 mediates histone methylation during cortical neuron generation. However, AF9 function and related mechanisms in human neurodevelopment remain unknown. Here we show that AF9 is necessary and sufficient for human embryonic stem cell (hESC) neural differentiation and neurodevelopmental gene activation. The 5-methylcytosine (5mC) dioxygenase TET2, which was identified in an AF9-associated protein complex, physically interacted with AF9. Both AF9 and TET2 co-localized in 5-hydroxymethylcytosine (5hmC)-positive hESC-derived neurons and were required for appropriate hESC neural differentiation. Upon binding to AAC-containing motifs, AF9 recruited TET2 to occupy the common neurodevelopmental gene loci to direct 5mC-to-5hmC conversion, which was followed by sequential activation of neural target genes and hESC neural commitment. These findings define an AF9-TET2 regulatory complex for modulating human neural development and reveal a novel mechanism by which the AF9 recognition specificity and TET2 hydroxylation activity cooperate to control neurodevelopmental gene activation.
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Affiliation(s)
- Yunbo Qiao
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, China
| | - Xiongjun Wang
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine , Shanghai, China
| | - Ran Wang
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, China
| | - Yuanyuan Li
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, China
| | - Fang Yu
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, China
| | - Xianfa Yang
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Lu Song
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, China
| | - Guoliang Xu
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, China
| | - Y Eugene Chin
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine , Shanghai, China
| | - Naihe Jing
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, China
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261
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TET proteins in cancer: Current 'state of the art'. Crit Rev Oncol Hematol 2015; 96:425-36. [PMID: 26276226 DOI: 10.1016/j.critrevonc.2015.07.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Revised: 05/26/2015] [Accepted: 07/16/2015] [Indexed: 12/31/2022] Open
Abstract
Aberrations in DNA methylation patterns are observed from the early stages of carcinogenesis. However, the mechanisms that drive these changes remain elusive. The recent characterization of ten-eleven translocation (TET) enzymes as a source of newly modified cytosines (5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine) has shed new light on the DNA demethylation process. These cytosines are intermediates of an active DNA demethylation process and are epigenetic markers per se. In this review, we discuss the mechanism and function of TET proteins in biological processes as well as current knowledge regarding their expression and regulation in cancer.
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262
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Kubik G, Summerer D. Deciphering Epigenetic Cytosine Modifications by Direct Molecular Recognition. ACS Chem Biol 2015; 10:1580-9. [PMID: 25897631 DOI: 10.1021/acschembio.5b00158] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Epigenetic modification at the 5-position of cytosine is a key regulatory element of mammalian gene expression with important roles in genome stability, development, and disease. The repertoire of cytosine modifications has long been confined to only 5-methylcytosine (mC) but has recently been expanded by the discovery of 5-hydroxymethyl-, 5-formyl-, and 5-carboxylcytosine. These are key intermediates of active mC demethylation but may additionally represent new epigenetic marks with distinct biological roles. This leap in chemical complexity of epigenetic cytosine modifications has not only created a pressing need for analytical approaches that enable unraveling of their functions, it has also created new challenges for such analyses with respect to sensitivity and selectivity. The crucial step of any such approach that defines its analytic potential is the strategy used for the actual differentiation of the cytosine 5-modifications from one another, and this selectivity can in principle be provided either by chemoselective conversions or by selective, molecular recognition events. While the former strategy has been particularly successful for accurate genomic profiling of cytosine modifications in vitro, the latter strategy provides interesting perspectives for simplified profiling of natural, untreated DNA, as well as for emerging applications such as single cell analysis and the monitoring of cytosine modification in vivo. We here review analytical techniques for the deciphering of epigenetic cytosine modifications with an emphasis on approaches that are based on the direct molecular recognition of these modifications in DNA.
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Affiliation(s)
- Grzegorz Kubik
- Department of Chemistry,
Zukunftskolleg, and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Daniel Summerer
- Department of Chemistry,
Zukunftskolleg, and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
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263
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Hashimoto H, Zhang X, Vertino PM, Cheng X. The Mechanisms of Generation, Recognition, and Erasure of DNA 5-Methylcytosine and Thymine Oxidations. J Biol Chem 2015; 290:20723-20733. [PMID: 26152719 DOI: 10.1074/jbc.r115.656884] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
One of the most fundamental questions in the control of gene expression in mammals is how the patterns of epigenetic modifications of DNA are generated, recognized, and erased. This includes covalent cytosine methylation of DNA and its associated oxidation states. An array of AdoMet-dependent methyltransferases, Fe(II)- and α-ketoglutarate-dependent dioxygenases, base excision glycosylases, and sequence-specific transcription factors is responsible for changing, maintaining, and interpreting the modification status of specific regions of chromatin. This review focuses on recent developments in characterizing the functional and structural links between the modification status of two DNA bases 5-methylcytosine and thymine (5-methyluracil).
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Affiliation(s)
- Hideharu Hashimoto
- Departments of Biochemistry, Emory University School of Medicine, Emory University, Atlanta, Georgia 30322
| | - Xing Zhang
- Departments of Biochemistry, Emory University School of Medicine, Emory University, Atlanta, Georgia 30322
| | - Paula M Vertino
- Departments of Radiation Oncology, Emory University School of Medicine, Emory University, Atlanta, Georgia 30322; Winship Cancer Institute, Emory University, Atlanta, Georgia 30322
| | - Xiaodong Cheng
- Departments of Biochemistry, Emory University School of Medicine, Emory University, Atlanta, Georgia 30322; Winship Cancer Institute, Emory University, Atlanta, Georgia 30322.
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264
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Pan F, Weeks O, Yang FC, Xu M. The TET2 interactors and their links to hematological malignancies. IUBMB Life 2015; 67:438-45. [PMID: 26099018 DOI: 10.1002/iub.1389] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 05/14/2015] [Indexed: 12/19/2022]
Abstract
Ten-eleven translocation (TET) family proteins are dioxygenases that oxidize 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine in DNA, early steps of active DNA demethylation. TET2, the second member of TET protein family, is frequently mutated in patients with hematological malignancies, leading to aberrant DNA methylation profiling and decreased 5hmC levels. Located in the nucleus and acting as a DNA-modifying enzyme, TET2 is thought to exert its function via TET2-containing protein complexes. Identifying the interactome network of TET2 likely holds the key to uncover the mechanisms by which TET2 exerts its function in cells. Here, we review recent literature on TET2 interactors and discuss their possible roles in TET2 loss-mediated dysregulation of hematopoiesis and pathogenesis of hematological malignancies.
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Affiliation(s)
- Feng Pan
- Department of Biological Sciences, Florida International University, Miami, FL, USA.,Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Ophelia Weeks
- Department of Biological Sciences, Florida International University, Miami, FL, USA
| | - Feng-Chun Yang
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, USA.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Mingjiang Xu
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, USA.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
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265
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Abstract
DNA methylation is a chemical modification that occurs predominantly on CG dinucleotides in mammalian genomes. However, recent studies have revealed that non-CG methylation (mCH) is abundant and nonrandomly distributed in the genomes of pluripotent cells and brain cells, and is present at lower levels in many other human cells and tissues. Surprisingly, mCH in pluripotent cells is distinct from that in brain cells in terms of sequence specificity and association with transcription, indicating the existence of different mCH pathways. In addition, several recent studies have begun to reveal the biological significance of mCH in diverse cellular processes. In reprogrammed somatic cells, mCH marks megabase-scale regions that have failed to revert to the pluripotent epigenetic state. In myocytes, promoter mCH accumulation is associated with the transcriptional response to environmental factors. In brain cells, mCH accumulates during the establishment of neural circuits and is associated with Rett syndrome. In this review, we summarize the current understanding of mCH and its possible functional consequences in different biological contexts.
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Affiliation(s)
- Yupeng He
- Bioinformatics Program, University of California, San Diego, La Jolla, California 92093
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266
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Lee LA, Arvai KJ, Jones D. Annotation of Sequence Variants in Cancer Samples: Processes and Pitfalls for Routine Assays in the Clinical Laboratory. J Mol Diagn 2015; 17:339-51. [PMID: 25977238 DOI: 10.1016/j.jmoldx.2015.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 03/12/2015] [Accepted: 03/23/2015] [Indexed: 12/16/2022] Open
Abstract
As DNA sequencing of multigene panels becomes routine for cancer samples in the clinical laboratory, an efficient process for classifying variants has become more critical. Determining which germline variants are significant for cancer disposition and which somatic mutations are integral to cancer development or therapy response remains difficult, even for well-studied genes such as BRCA1 and TP53. We compare and contrast the general principles and lines of evidence commonly used to distinguish the significance of cancer-associated germline and somatic genetic variants. The factors important in each step of the analysis pipeline are reviewed, as are some of the publicly available annotation tools. Given the range of indications and uses of cancer sequencing assays, including diagnosis, staging, prognostication, theranostics, and residual disease detection, the need for flexible methods for scoring of variants is discussed. The usefulness of protein prediction tools and multimodal risk-based or Bayesian approaches are highlighted. Using TET2 variants encountered in hematologic neoplasms, several examples of this multifactorial approach to classifying sequence variants of unknown significance are presented. Although there are still significant gaps in the publicly available data for many cancer genes that limit the broad application of explicit algorithms for variant scoring, the elements of a more rigorous model are outlined.
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Affiliation(s)
- Lobin A Lee
- Department of Pathology, Quest Diagnostics Nichols Institute, Chantilly, Virginia.
| | - Kevin J Arvai
- Department of Pathology, Quest Diagnostics Nichols Institute, Chantilly, Virginia
| | - Dan Jones
- Department of Pathology, Quest Diagnostics Nichols Institute, Chantilly, Virginia
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267
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Aravind L, Zhang D, Iyer LM. The TET/JBP Family of Nucleic Acid Base-Modifying 2-Oxoglutarate and Iron-Dependent Dioxygenases. 2-OXOGLUTARATE-DEPENDENT OXYGENASES 2015. [DOI: 10.1039/9781782621959-00289] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The TET/JBP family of enzymes includes 2-oxoglutarate- and Fe(ii)-dependent dioxygenases that oxidize 5-methylpyrimidines in nucleic acids. They include euglenozoan JBP enzymes that catalyse the first step in the biosynthesis of the hypermodified thymine, base J, and metazoan TET enzymes that generate oxidized 5-methylcytosines (hydroxy-, formyl- and carboxymethylcytosine) in DNA. Recent studies suggest that these modified bases function as epigenetic marks and/or as potential intermediates for DNA demethylation during resetting of epigenetic 5mC marks upon zygote formation and in primordial germ cell development. Studies in mammalian models also point to an important role for these enzymes in haematopoiesis, tumour suppression, cell differentiation and neural behavioural adaptation. The TET/JBP family has undergone extensive gene expansion in fungi, such as mushrooms, in conjunction with a novel class of transposons and might play a role in genomic plasticity and speciation. Certain versions from stramenopiles and chlorophytes are likely to modify RNA and often show fusions to other RNA-modifying enzymatic domains. The ultimate origin of the TET/JBP family lies in bacteriophages where the enzymes are likely to catalyse formation of modified bases with key roles in DNA packaging and evasion of host restriction.
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Affiliation(s)
- L. Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda MD 20894 USA
| | - Dapeng Zhang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda MD 20894 USA
| | - Lakshminarayan M. Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda MD 20894 USA
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268
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Mahfoudhi E, Secardin L, Scourzic L, Bernard O, Vainchenker W, Plo I. Propriétés et rôles biologiques des protéines TET au cours du développement et de l’hématopoïèse. Med Sci (Paris) 2015; 31:268-74. [DOI: 10.1051/medsci/20153103012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
La méthylation de l’ADN est associée à de nombreux processus biologiques et concerne la méthylation de la cytosine en position 5 (5-mC). Un mécanisme actif de déméthylation, jusqu’alors discuté, a été mis en évidence en 2009 à la suite de la découverte des protéines TET (ten-eleven-translocation). Ces protéines sont des enzymes capables d’hydroxyler la 5-mC en 5-hydroxyméthylcytosine. Simultanément, d’autres études ont montré la fréquence et le rôle des mutations acquises de TET2 dans les hémopathies et leur pathogenèse. Depuis, ces protéines ont été impliquées dans de très nombreux processus, ouvrant un nouveau domaine de recherche. Dans cette revue, nous discuterons les fonctions enzymatique et biologique de ces protéines, ainsi que leurs rôles, notamment au cours de l’hématopoïèse et du développement.
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269
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Li Z, Gu TP, Weber AR, Shen JZ, Li BZ, Xie ZG, Yin R, Guo F, Liu X, Tang F, Wang H, Schär P, Xu GL. Gadd45a promotes DNA demethylation through TDG. Nucleic Acids Res 2015; 43:3986-97. [PMID: 25845601 PMCID: PMC4417182 DOI: 10.1093/nar/gkv283] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Accepted: 03/23/2015] [Indexed: 11/25/2022] Open
Abstract
Growth arrest and DNA-damage-inducible protein 45 (Gadd45) family members have been implicated in DNA demethylation in vertebrates. However, it remained unclear how they contribute to the demethylation process. Here, we demonstrate that Gadd45a promotes active DNA demethylation through thymine DNA glycosylase (TDG) which has recently been shown to excise 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) generated in Ten-eleven-translocation (Tet)—initiated oxidative demethylation. The connection of Gadd45a with oxidative demethylation is evidenced by the enhanced activation of a methylated reporter gene in HEK293T cells expressing Gadd45a in combination with catalytically active TDG and Tet. Gadd45a interacts with TDG physically and increases the removal of 5fC and 5caC from genomic and transfected plasmid DNA by TDG. Knockout of both Gadd45a and Gadd45b from mouse ES cells leads to hypermethylation of specific genomic loci most of which are also targets of TDG and show 5fC enrichment in TDG-deficient cells. These observations indicate that the demethylation effect of Gadd45a is mediated by TDG activity. This finding thus unites Gadd45a with the recently defined Tet-initiated demethylation pathway.
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Affiliation(s)
- Zheng Li
- Group of DNA Metabolism, The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Tian-Peng Gu
- Group of DNA Metabolism, The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Alain R Weber
- Department of Biomedicine, University of Basel, Basel 4048, Switzerland
| | - Jia-Zhen Shen
- Group of DNA Metabolism, The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bin-Zhong Li
- Group of DNA Metabolism, The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhi-Guo Xie
- Group of DNA Metabolism, The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ruichuan Yin
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Fan Guo
- Biodynamic Optical Imaging Center, College of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaomeng Liu
- Biodynamic Optical Imaging Center, College of Life Sciences, Peking University, Beijing 100871, China
| | - Fuchou Tang
- Biodynamic Optical Imaging Center, College of Life Sciences, Peking University, Beijing 100871, China Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Peking University, Beijing 100871, China
| | - Hailin Wang
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Primo Schär
- Department of Biomedicine, University of Basel, Basel 4048, Switzerland
| | - Guo-Liang Xu
- Group of DNA Metabolism, The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China School of Life Science and Technology, ShanghaiTech University, 319 Yue Yang Road, Shanghai 200031, China
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270
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Biochemical characterization of a Naegleria TET-like oxygenase and its application in single molecule sequencing of 5-methylcytosine. Proc Natl Acad Sci U S A 2015; 112:4316-21. [PMID: 25831492 DOI: 10.1073/pnas.1417939112] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Modified DNA bases in mammalian genomes, such as 5-methylcytosine ((5m)C) and its oxidized forms, are implicated in important epigenetic regulation processes. In human or mouse, successive enzymatic conversion of (5m)C to its oxidized forms is carried out by the ten-eleven translocation (TET) proteins. Previously we reported the structure of a TET-like (5m)C oxygenase (NgTET1) from Naegleria gruberi, a single-celled protist evolutionarily distant from vertebrates. Here we show that NgTET1 is a 5-methylpyrimidine oxygenase, with activity on both (5m)C (major activity) and thymidine (T) (minor activity) in all DNA forms tested, and provide unprecedented evidence for the formation of 5-formyluridine ((5f)U) and 5-carboxyuridine ((5ca)U) in vitro. Mutagenesis studies reveal a delicate balance between choice of (5m)C or T as the preferred substrate. Furthermore, our results suggest substrate preference by NgTET1 to (5m)CpG and TpG dinucleotide sites in DNA. Intriguingly, NgTET1 displays higher T-oxidation activity in vitro than mammalian TET1, supporting a closer evolutionary relationship between NgTET1 and the base J-binding proteins from trypanosomes. Finally, we demonstrate that NgTET1 can be readily used as a tool in (5m)C sequencing technologies such as single molecule, real-time sequencing to map (5m)C in bacterial genomes at base resolution.
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271
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Reading the unique DNA methylation landscape of the brain: Non-CpG methylation, hydroxymethylation, and MeCP2. Proc Natl Acad Sci U S A 2015; 112:6800-6. [PMID: 25739960 DOI: 10.1073/pnas.1411269112] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
DNA methylation at CpG dinucleotides is an important epigenetic regulator common to virtually all mammalian cell types, but recent evidence indicates that during early postnatal development neuronal genomes also accumulate uniquely high levels of two alternative forms of methylation, non-CpG methylation and hydroxymethylation. Here we discuss the distinct landscape of DNA methylation in neurons, how it is established, and how it might affect the binding and function of protein readers of DNA methylation. We review studies of one critical reader of DNA methylation in the brain, the Rett syndrome protein methyl CpG-binding protein 2 (MeCP2), and discuss how differential binding affinity of MeCP2 for non-CpG and hydroxymethylation may affect the function of this methyl-binding protein in the nervous system.
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272
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Lu X, Zhao BS, He C. TET family proteins: oxidation activity, interacting molecules, and functions in diseases. Chem Rev 2015; 115:2225-39. [PMID: 25675246 DOI: 10.1021/cr500470n] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Xingyu Lu
- †Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States.,‡Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Boxuan Simen Zhao
- †Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States.,‡Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Chuan He
- †Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States.,‡Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
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273
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Shen L, Song CX, He C, Zhang Y. Mechanism and function of oxidative reversal of DNA and RNA methylation. Annu Rev Biochem 2015; 83:585-614. [PMID: 24905787 DOI: 10.1146/annurev-biochem-060713-035513] [Citation(s) in RCA: 246] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The importance of eukaryotic DNA methylation [5-methylcytosine (5mC)] in transcriptional regulation and development was first suggested almost 40 years ago. However, the molecular mechanism underlying the dynamic nature of this epigenetic mark was not understood until recently, following the discovery that the TET proteins, a family of AlkB-like Fe(II)/α-ketoglutarate-dependent dioxygenases, can oxidize 5mC to generate 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). Since then, several mechanisms that are responsible for processing oxidized 5mC derivatives to achieve DNA demethylation have emerged. Our biochemical understanding of the DNA demethylation process has prompted new investigations into the biological functions of DNA demethylation. Characterization of two additional AlkB family proteins, FTO and ALKBH5, showed that they possess demethylase activity toward N(6)-methyladenosine (m(6)A) in RNA, indicating that members of this subfamily of dioxygenases have a general function in demethylating nucleic acids. In this review, we discuss recent advances in this emerging field, focusing on the mechanism and function of TET-mediated DNA demethylation.
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Affiliation(s)
- Li Shen
- Howard Hughes Medical Institute and
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274
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Bauer C, Göbel K, Nagaraj N, Colantuoni C, Wang M, Müller U, Kremmer E, Rottach A, Leonhardt H. Phosphorylation of TET proteins is regulated via O-GlcNAcylation by the O-linked N-acetylglucosamine transferase (OGT). J Biol Chem 2015; 290:4801-4812. [PMID: 25568311 PMCID: PMC4335217 DOI: 10.1074/jbc.m114.605881] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
TET proteins oxidize 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine and thus provide a possible means for active DNA demethylation in mammals. Although their catalytic mechanism is well characterized and the catalytic dioxygenase domain is highly conserved, the function of the regulatory regions (the N terminus and the low-complexity insert between the two parts of the dioxygenase domains) is only poorly understood. Here, we demonstrate that TET proteins are subject to a variety of post-translational modifications that mostly occur at these regulatory regions. We mapped TET modification sites at amino acid resolution and show for the first time that TET1, TET2, and TET3 are highly phosphorylated. The O-linked GlcNAc transferase, which we identified as a strong interactor with all three TET proteins, catalyzes the addition of a GlcNAc group to serine and threonine residues of TET proteins and thereby decreases both the number of phosphorylation sites and site occupancy. Interestingly, the different TET proteins display unique post-translational modification patterns, and some modifications occur in distinct combinations. In summary, our results provide a novel potential mechanism for TET protein regulation based on a dynamic interplay of phosphorylation and O-GlcNAcylation at the N terminus and the low-complexity insert region. Our data suggest strong cross-talk between the modification sites that could allow rapid adaption of TET protein localization, activity, or targeting due to changing environmental conditions as well as in response to external stimuli.
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Affiliation(s)
- Christina Bauer
- Biocenter, Ludwig-Maximilians University Munich, 82152 Planegg-Martinsried
| | - Klaus Göbel
- Biocenter, Ludwig-Maximilians University Munich, 82152 Planegg-Martinsried
| | | | | | - Mengxi Wang
- Biocenter, Ludwig-Maximilians University Munich, 82152 Planegg-Martinsried
| | - Udo Müller
- Biocenter, Ludwig-Maximilians University Munich, 82152 Planegg-Martinsried
| | - Elisabeth Kremmer
- Institute for Molecular Immunology, Helmholtz Center Munich, 81377 München-Groβhadern
| | - Andrea Rottach
- Biocenter, Ludwig-Maximilians University Munich, 82152 Planegg-Martinsried,.
| | - Heinrich Leonhardt
- Biocenter, Ludwig-Maximilians University Munich, 82152 Planegg-Martinsried,; Center for Integrated Protein Science Munich (CIPSM), 81377 München, Germany.
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275
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Raiber EA, Murat P, Chirgadze DY, Beraldi D, Luisi BF, Balasubramanian S. 5-Formylcytosine alters the structure of the DNA double helix. Nat Struct Mol Biol 2015; 22:44-49. [PMID: 25504322 PMCID: PMC4287393 DOI: 10.1038/nsmb.2936] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 11/21/2014] [Indexed: 12/15/2022]
Abstract
The modified base 5-formylcytosine (5fC) was recently identified in mammalian DNA and might be considered to be the 'seventh' base of the genome. This nucleotide has been implicated in active demethylation mediated by the base excision repair enzyme thymine DNA glycosylase. Genomics and proteomics studies have suggested an additional role for 5fC in transcription regulation through chromatin remodeling. Here we propose that 5fC might affect these processes through its effect on DNA conformation. Biophysical and structural analysis revealed that 5fC alters the structure of the DNA double helix and leads to a conformation unique among known DNA structures including those comprising other cytosine modifications. The 1.4-Å-resolution X-ray crystal structure of a DNA dodecamer comprising three 5fCpG sites shows how 5fC changes the geometry of the grooves and base pairs associated with the modified base, leading to helical underwinding.
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Affiliation(s)
- Eun-Ang Raiber
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Pierre Murat
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | - Dario Beraldi
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
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276
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Nakagawa T, Lv L, Nakagawa M, Yu Y, Yu C, D'Alessio AC, Nakayama K, Fan HY, Chen X, Xiong Y. CRL4(VprBP) E3 ligase promotes monoubiquitylation and chromatin binding of TET dioxygenases. Mol Cell 2014; 57:247-260. [PMID: 25557551 DOI: 10.1016/j.molcel.2014.12.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 08/26/2014] [Accepted: 11/24/2014] [Indexed: 12/17/2022]
Abstract
DNA methylation at the C-5 position of cytosine (5mC) regulates gene expression and plays pivotal roles in various biological processes. The TET dioxygenases catalyze iterative oxidation of 5mC, leading to eventual demethylation. Inactivation of TET enzymes causes multistage developmental defects, impaired cell reprogramming, and hematopoietic malignancies. However, little is known about how TET activity is regulated. Here we show that all three TET proteins bind to VprBP and are monoubiquitylated by the VprBP-DDB1-CUL4-ROC1 E3 ubiquitin ligase (CRL4(VprBP)) on a highly conserved lysine residue. Deletion of VprBP in oocytes abrogated paternal DNA hydroxymethylation in zygotes. VprBP-mediated monoubiquitylation promotes TET binding to chromatin. Multiple recurrent TET2-inactivating mutations derived from leukemia target either the monoubiquitylation site (K1299) or residues essential for VprBP binding. Cumulatively, our data demonstrate that CRL4(VprBP) is a critical regulator of TET dioxygenases during development and in tumor suppression.
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Affiliation(s)
- Tadashi Nakagawa
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Lei Lv
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Makiko Nakagawa
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Yanbao Yu
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Chao Yu
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Ana C D'Alessio
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Keiko Nakayama
- Division of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai 980-8575, Japan
| | - Heng-Yu Fan
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xian Chen
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Yue Xiong
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, NC 27599, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC 27599, USA
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277
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14-3-3 tau (YWHAQ) gene promoter hypermethylation in human placenta of preeclampsia. Placenta 2014; 35:981-8. [DOI: 10.1016/j.placenta.2014.09.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/06/2014] [Accepted: 09/22/2014] [Indexed: 12/16/2022]
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278
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Single-base resolution analysis of active DNA demethylation using methylase-assisted bisulfite sequencing. Nat Biotechnol 2014; 32:1231-40. [PMID: 25362244 PMCID: PMC4269366 DOI: 10.1038/nbt.3073] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Accepted: 10/15/2014] [Indexed: 12/20/2022]
Abstract
Active DNA demethylation in mammals involves TET-mediated iterative oxidation of 5-methylcytosine (5mC)/5-hydroxymethylcytosine (5hmC) and subsequent excision repair of highly oxidized cytosine bases 5-formylcytosine (5fC)/5-carboxylcytosine (5caC) by thymine DNA glycosylase (TDG). However, quantitative and high-resolution analysis of active DNA demethylation activity remains challenging. Here, we describe M.SssI methylase-assisted bisulfite sequencing (MAB-seq), a method that directly maps 5fC/5caC at single-base resolution. Genome-wide MAB-seq allows systematic identification of 5fC/5caC in Tdg-depleted embryonic stem cells, thereby generating a base-resolution map of active DNA demethylome. A comparison of 5fC/5caC and 5hmC distribution maps indicates that catalytic processivity of TET enzymes correlates with local chromatin accessibility. MAB-seq also reveals strong strand asymmetry of active demethylation within palindromic CpGs. Integrating MAB-seq with other base-resolution mapping methods enables quantitative measurement of cytosine modification states at key transitioning steps of the active DNA demethylation cascade and reveals a regulatory role of 5fC/5caC excision repair in this step-wise process.
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279
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Dong C, Zhang H, Xu C, Arrowsmith CH, Min J. Structure and function of dioxygenases in histone demethylation and DNA/RNA demethylation. IUCRJ 2014; 1:540-9. [PMID: 25485134 PMCID: PMC4224472 DOI: 10.1107/s2052252514020922] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 09/18/2014] [Indexed: 05/18/2023]
Abstract
Iron(II) and 2-oxoglutarate (2OG)-dependent dioxygenases involved in histone and DNA/RNA demethylation convert the cosubstrate 2OG and oxygen to succinate and carbon dioxide, resulting in hydroxylation of the methyl group of the substrates and subsequent demethylation. Recent evidence has shown that these 2OG dioxygenases play vital roles in a variety of biological processes, including transcriptional regulation and gene expression. In this review, the structure and function of these dioxygenases in histone and nucleic acid demethylation will be discussed. Given the important roles of these 2OG dioxygenases, detailed analysis and comparison of the 2OG dioxygenases will guide the design of target-specific small-molecule chemical probes and inhibitors.
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Affiliation(s)
- Cheng Dong
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Heng Zhang
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Chao Xu
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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280
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Hashimoto H. Structural and mutation studies of two DNA demethylation related glycosylases: MBD4 and TDG. Biophysics (Nagoya-shi) 2014; 10:63-8. [PMID: 27493500 PMCID: PMC4629659 DOI: 10.2142/biophysics.10.63] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 09/23/2014] [Indexed: 12/01/2022] Open
Abstract
Two mammalian DNA glycosylases, methyl-CpG binding domain protein 4 (MBD4) and thymine DNA glycosylase (TDG), are involved in active DNA demethylation via the base excision repair pathway. Both MBD4 and TDG excise the mismatch base from G:X, where X is uracil, thymine, and 5-hydroxymethyluracil (5hmU). In addition, TDG excises 5mC oxidized bases i.e. when X is 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) not 5-hydroxymethylcytosine (5hmC). A MBD4 inactive mutant and substrate crystal structure clearly explains how MBD4 glycosylase discriminates substrates: 5mC are not able to be directly excised, but a deamination process from 5mC to thymine is required. On the other hand, TDG is much more complicated; in this instance, crystal structures show that TDG recognizes G:X mismatch DNA containing DNA and G:5caC containing DNA from the minor groove of DNA, which suggested that TDG might recognize 5mC oxidized product 5caC like mismatch DNA. In mutation studies, a N157D mutation results in a more 5caC specific glycosylase, and a N191A mutation inhibits 5caC activity while that when X=5fC or T remains. Here I revisit the recent MBD4 glycos ylase domain co-crystal structures with DNA, as well as TDG glycosylase domain co-crystal structures with DNA in conjunction with its mutation studies.
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Affiliation(s)
- Hideharu Hashimoto
- Department of Biochemistry, Emory University, 1510 Clifton Road, Atlanta Georgia 30322, USA
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281
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Day JJ, Kennedy AJ, Sweatt JD. DNA methylation and its implications and accessibility for neuropsychiatric therapeutics. Annu Rev Pharmacol Toxicol 2014; 55:591-611. [PMID: 25340930 DOI: 10.1146/annurev-pharmtox-010814-124527] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this review, we discuss the potential pharmacological targeting of a set of powerful epigenetic mechanisms: DNA methylation control systems in the central nervous system (CNS). Specifically, we focus on the possible use of these targets for novel future treatments for learning and memory disorders. We first describe several unique pharmacological attributes of epigenetic mechanisms, especially DNA cytosine methylation, as potential drug targets. We then present an overview of the existing literature regarding DNA methylation control pathways and enzymes in the nervous system, particularly as related to synaptic function, plasticity, learning and memory. Lastly, we speculate upon potential categories of CNS cognitive disorders that might be amenable to methylomic targeting.
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Affiliation(s)
- Jeremy J Day
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama 35294; , ,
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282
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Huang Y, Rao A. Connections between TET proteins and aberrant DNA modification in cancer. Trends Genet 2014; 30:464-74. [PMID: 25132561 PMCID: PMC4337960 DOI: 10.1016/j.tig.2014.07.005] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 07/24/2014] [Accepted: 07/24/2014] [Indexed: 02/07/2023]
Abstract
DNA methylation has been linked to aberrant silencing of tumor suppressor genes in cancer, and an imbalance in DNA methylation-demethylation cycles is intimately implicated in the onset and progression of tumors. Ten-eleven translocation (TET) proteins are Fe(II)- and 2-oxoglutarate (2OG)-dependent dioxygenases that successively oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), thereby mediating active DNA demethylation. In this review, we focus on the pathophysiological role of TET proteins and 5hmC in cancer. We present an overview of loss-of-function mutations and abnormal expression and regulation of TET proteins in hematological malignancies and solid tumors, and discuss the potential prognostic value of assessing TET mutations and 5hmC levels in cancer patients. We also address the crosstalk between TET and two critical enzymes involved in cell metabolism: O-linked β-N-acetylglucosamine transferase (OGT) and isocitrate dehydrogenase (IDH). Lastly, we discuss the therapeutic potential of targeting TET proteins and aberrant DNA methylation in cancer.
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Affiliation(s)
- Yun Huang
- La Jolla Institute, La Jolla, CA 92037, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA.
| | - Anjana Rao
- La Jolla Institute, La Jolla, CA 92037, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA.
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283
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Lu F, Liu Y, Jiang L, Yamaguchi S, Zhang Y. Role of Tet proteins in enhancer activity and telomere elongation. Genes Dev 2014; 28:2103-19. [PMID: 25223896 PMCID: PMC4180973 DOI: 10.1101/gad.248005.114] [Citation(s) in RCA: 203] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Using CRISPR/Cas9 technology, Lu et al. generated mouse embryonic stem cells (ESCs) that are deficient for all three Tet proteins. Functional characterization of these ESCs revealed a role for Tet proteins in regulating the two-cell embryo (2C)-like state under ESC culture conditions. The knockout ESCs exhibited increased telomere–sister chromatid exchange and elongated telomeres. DNA methylation at the C-5 position of cytosine (5mC) is one of the best-studied epigenetic modifications and plays important roles in diverse biological processes. Iterative oxidation of 5mC by the ten-eleven translocation (Tet) family of proteins generates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC and 5caC are selectively recognized and excised by thymine DNA glycosylase (TDG), leading to DNA demethylation. Functional characterization of Tet proteins has been complicated by the redundancy between the three family members. Using CRISPR/Cas9 technology, we generated mouse embryonic stem cells (ESCs) deficient for all three Tet proteins (Tet triple knockout [TKO]). Whole-genome bisulfite sequencing (WGBS) analysis revealed that Tet-mediated DNA demethylation mainly occurs at distally located enhancers and fine-tunes the transcription of genes associated with these regions. Functional characterization of Tet TKO ESCs revealed a role for Tet proteins in regulating the two-cell embryo (2C)-like state under ESC culture conditions. In addition, Tet TKO ESCs exhibited increased telomere–sister chromatid exchange and elongated telomeres. Collectively, our study reveals a role for Tet proteins in not only DNA demethylation at enhancers but also regulating the 2C-like state and telomere homeostasis.
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Affiliation(s)
- Falong Lu
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Yuting Liu
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Lan Jiang
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Shinpei Yamaguchi
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Harvard Stem Cell Institute, Boston, Massachusetts 02115, USA
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284
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Xu L, Chen YC, Chong J, Fin A, McCoy LS, Xu J, Zhang C, Wang D. Pyrene-based quantitative detection of the 5-formylcytosine loci symmetry in the CpG duplex content during TET-dependent demethylation. Angew Chem Int Ed Engl 2014; 53:11223-7. [PMID: 25159856 DOI: 10.1002/anie.201406220] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 07/21/2014] [Indexed: 01/19/2023]
Abstract
Methylcytosine (5mC) is mostly symmetrically distributed in CpG sites. Ten-eleven-translocation (TET) proteins are the key enzymes involved in active DNA demethylation through stepwise oxidation of 5mC. However, oxidation pathways of TET enzymes in the symmetrically methylated CpG context are still elusive. Employing the unique fluorescence properties of pyrene group, we designed and synthesized a sensitive fluorescence-based probe not only to target 5-formylcytosine (5fC) sites, but also to distinguish symmetric from asymmetric 5fC sites in the double stranded DNA context during TET-dependent 5mC oxidation process. Using this novel probe, we revealed dominant levels of symmetric 5fC among total 5fC sites during in vitro TET-dependent 5mC oxidation and novel mechanistic insights into the TET-dependent 5mC oxidation in the mCpG context.
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Affiliation(s)
- Liang Xu
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 (USA)
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285
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Xu L, Chen YC, Chong J, Fin A, McCoy LS, Xu J, Zhang C, Wang D. Pyrene-Based Quantitative Detection of the 5-Formylcytosine Loci Symmetry in the CpG Duplex Content during TET-Dependent Demethylation. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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286
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Qiao Y, Quinlan AR, Jazaeri AA, Verhaak RG, Wheeler DA, Marth GT. SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization. Genome Biol 2014; 15:443. [PMID: 25160522 PMCID: PMC4180956 DOI: 10.1186/s13059-014-0443-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 07/31/2014] [Indexed: 01/03/2023] Open
Abstract
Many tumors are composed of genetically divergent cell subpopulations. We report SubcloneSeeker, a package capable of exhaustive identification of subclone structures and evolutionary histories with bulk somatic variant allele frequency measurements from tumor biopsies. We present a statistical framework to elucidate whether specific sets of mutations are present within the same subclones, and the order in which they occur. We demonstrate how subclone reconstruction provides crucial information about tumorigenesis and relapse mechanisms; guides functional study by variant prioritization, and has the potential as a rational basis for informed therapeutic strategies for the patient. SubcloneSeeker is available at: https://github.com/yiq/SubcloneSeeker.
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287
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Dnmt3a regulates global gene expression in olfactory sensory neurons and enables odorant-induced transcription. Neuron 2014; 83:823-38. [PMID: 25123312 DOI: 10.1016/j.neuron.2014.07.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2014] [Indexed: 12/11/2022]
Abstract
During differentiation, neurons exhibit a reorganization of DNA modification patterns across their genomes. The de novo DNA methyltransferase Dnmt3a is implicated in this process, but the effects of its absence have not been fully characterized in a purified neuronal population. To better understand how DNA modifications contribute to neuronal function, we performed a comprehensive analysis of the epigenetic and transcriptional landscapes of Dnmt3a-deficient mature olfactory sensory neurons (mOSNs), the primary sensory neurons of the olfactory epithelium. Dnmt3a is required for both 5-methylcytosine and 5-hydroxymethylcytosine patterning within accessible genomic regions, including hundreds of neurodevelopmental genes and neural enhancers. Loss of Dnmt3a results in the global disruption of gene expression via activation of silent genes and reduction of mOSN-expressed transcripts. Importantly, the DNA modification state and inducibility of odorant-activated genes are markedly impaired in Dnmt3a knockouts, suggesting a crucial role for this enzyme in establishing an epigenetic landscape compatible with neuronal plasticity.
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288
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Fu L, Guerrero CR, Zhong N, Amato NJ, Liu Y, Liu S, Cai Q, Ji D, Jin SG, Niedernhofer LJ, Pfeifer GP, Xu GL, Wang Y. Tet-mediated formation of 5-hydroxymethylcytosine in RNA. J Am Chem Soc 2014; 136:11582-5. [PMID: 25073028 PMCID: PMC4140497 DOI: 10.1021/ja505305z] [Citation(s) in RCA: 256] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Oxidation of 5-methylcytosine
in DNA by ten-eleven translocation
(Tet) family of enzymes has been demonstrated to play a significant
role in epigenetic regulation in mammals. We found that Tet enzymes
also possess the activity of catalyzing the formation of 5-hydroxymethylcytidine
(5-hmrC) in RNA in vitro. In addition, the catalytic
domains of all three Tet enzymes as well as full-length Tet3 could
induce the formation of 5-hmrC in human cells. Moreover, 5-hmrC was
present at appreciable levels (∼1 per 5000 5-methylcytidine)
in RNA of mammalian cells and tissues. Our results suggest the involvement
of this oxidation in RNA biology.
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Affiliation(s)
- Lijuan Fu
- Environmental Toxicology Graduate Program and ‡Department of Chemistry, University of California , Riverside, California 92521, United States
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289
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Zhang D, Iyer LM, Burroughs AM, Aravind L. Resilience of biochemical activity in protein domains in the face of structural divergence. Curr Opin Struct Biol 2014; 26:92-103. [PMID: 24952217 DOI: 10.1016/j.sbi.2014.05.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 05/20/2014] [Indexed: 01/07/2023]
Abstract
Recent studies point to the prevalence of the evolutionary phenomenon of drastic structural transformation of protein domains while continuing to preserve their basic biochemical function. These transformations span a wide spectrum, including simple domains incorporated into larger structural scaffolds, changes in the structural core, major active site shifts, topological rewiring and extensive structural transmogrifications. Proteins from biological conflict systems, such as toxin-antitoxin, restriction-modification, CRISPR/Cas, polymorphic toxin and secondary metabolism systems commonly display such transformations. These include endoDNases, metal-independent RNases, deaminases, ADP ribosyltransferases, immunity proteins, kinases and E1-like enzymes. In eukaryotes such transformations are seen in domains involved in chromatin-related peptide recognition and protein/DNA-modification. Intense selective pressures from 'arms-race'-like situations in conflict and macromolecular modification systems could favor drastic structural divergence while preserving function.
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Affiliation(s)
- Dapeng Zhang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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290
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Lu L, Zhu C, Xia B, Yi C. Oxidative Demethylation of DNA and RNA Mediated by Non-Heme Iron-Dependent Dioxygenases. Chem Asian J 2014; 9:2018-29. [DOI: 10.1002/asia.201402148] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Indexed: 11/10/2022]
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291
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Horton JR, Borgaro JG, Griggs RM, Quimby A, Guan S, Zhang X, Wilson GG, Zheng Y, Zhu Z, Cheng X. Structure of 5-hydroxymethylcytosine-specific restriction enzyme, AbaSI, in complex with DNA. Nucleic Acids Res 2014; 42:7947-59. [PMID: 24895434 PMCID: PMC4081097 DOI: 10.1093/nar/gku497] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AbaSI, a member of the PvuRts1I-family of modification-dependent restriction endonucleases, cleaves deoxyribonucleic acid (DNA) containing 5-hydroxymethylctosine (5hmC) and glucosylated 5hmC (g5hmC), but not DNA containing unmodified cytosine. AbaSI has been used as a tool for mapping the genomic locations of 5hmC, an important epigenetic modification in the DNA of higher organisms. Here we report the crystal structures of AbaSI in the presence and absence of DNA. These structures provide considerable, although incomplete, insight into how this enzyme acts. AbaSI appears to be mainly a homodimer in solution, but interacts with DNA in our structures as a homotetramer. Each AbaSI subunit comprises an N-terminal, Vsr-like, cleavage domain containing a single catalytic site, and a C-terminal, SRA-like, 5hmC-binding domain. Two N-terminal helices mediate most of the homodimer interface. Dimerization brings together the two catalytic sites required for double-strand cleavage, and separates the 5hmC binding-domains by ∼70 Å, consistent with the known activity of AbaSI which cleaves DNA optimally between symmetrically modified cytosines ∼22 bp apart. The eukaryotic SET and RING-associated (SRA) domains bind to DNA containing 5-methylcytosine (5mC) in the hemi-methylated CpG sequence. They make contacts in both the major and minor DNA grooves, and flip the modified cytosine out of the helix into a conserved binding pocket. In contrast, the SRA-like domain of AbaSI, which has no sequence specificity, contacts only the minor DNA groove, and in our current structures the 5hmC remains intra-helical. A conserved, binding pocket is nevertheless present in this domain, suitable for accommodating 5hmC and g5hmC. We consider it likely, therefore, that base-flipping is part of the recognition and cleavage mechanism of AbaSI, but that our structures represent an earlier, pre-flipped stage, prior to actual recognition.
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Affiliation(s)
- John R Horton
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA
| | - Janine G Borgaro
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Rose M Griggs
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA
| | - Aine Quimby
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Shengxi Guan
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Xing Zhang
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA
| | | | - Yu Zheng
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Zhenyu Zhu
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA
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292
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Abstract
Methylation of the fifth carbon of cytosine was the first epigenetic modification to be discovered in DNA. Recently, three new DNA modifications have come to light: hydroxymethylcytosine, formylcytosine, and carboxylcytosine, all generated by oxidation of methylcytosine by Ten Eleven Translocation (TET) enzymes. These modifications can initiate full DNA demethylation, but they are also likely to participate, like methylcytosine, in epigenetic signalling per se. A scenario is emerging in which coordinated regulation at multiple levels governs the participation of TETs in a wide range of physiological functions, sometimes via a mechanism unrelated to their enzymatic activity. Although still under construction, a sophisticated picture is rapidly forming where, according to the function to be performed, TETs ensure epigenetic marking to create specific landscapes, and whose improper build-up can lead to diseases such as cancer and neurodegenerative disorders.
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Affiliation(s)
- Benjamin Delatte
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, Brussels, Belgium
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, Brussels, Belgium
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, Brussels, Belgium
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293
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Xu C, Liu K, Tempel W, Demetriades M, Aik W, Schofield CJ, Min J. Structures of human ALKBH5 demethylase reveal a unique binding mode for specific single-stranded N6-methyladenosine RNA demethylation. J Biol Chem 2014; 289:17299-311. [PMID: 24778178 DOI: 10.1074/jbc.m114.550350] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
N(6)-Methyladenosine (m(6)A) is the most prevalent internal RNA modification in eukaryotes. ALKBH5 belongs to the AlkB family of dioxygenases and has been shown to specifically demethylate m(6)A in single-stranded RNA. Here we report crystal structures of ALKBH5 in the presence of either its cofactors or the ALKBH5 inhibitor citrate. Catalytic assays demonstrate that the ALKBH5 catalytic domain can demethylate both single-stranded RNA and single-stranded DNA. We identify the TCA cycle intermediate citrate as a modest inhibitor of ALKHB5 (IC50, ∼488 μm). The structural analysis reveals that a loop region of ALKBH5 is immobilized by a disulfide bond that apparently excludes the binding of dsDNA to ALKBH5. We identify the m(6)A binding pocket of ALKBH5 and the key residues involved in m(6)A recognition using mutagenesis and ITC binding experiments.
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Affiliation(s)
- Chao Xu
- the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Ke Liu
- the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada, From the Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, China
| | - Wolfram Tempel
- the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Marina Demetriades
- the Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, United Kingdom, and
| | - WeiShen Aik
- the Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, United Kingdom, and
| | - Christopher J Schofield
- the Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, United Kingdom, and
| | - Jinrong Min
- the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada, From the Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, China, the Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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294
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Affiliation(s)
- Guanqun Zheng
- Department of Chemistry and
Institute for Biophysical Dynamics, The
University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United
States
| | - Ye Fu
- Department of Chemistry and
Institute for Biophysical Dynamics, The
University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United
States
| | - Chuan He
- Department of Chemistry and
Institute for Biophysical Dynamics, The
University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United
States
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295
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Wu H, Zhang Y. Reversing DNA methylation: mechanisms, genomics, and biological functions. Cell 2014; 156:45-68. [PMID: 24439369 DOI: 10.1016/j.cell.2013.12.019] [Citation(s) in RCA: 755] [Impact Index Per Article: 75.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Indexed: 12/28/2022]
Abstract
Methylation of cytosines in the mammalian genome represents a key epigenetic modification and is dynamically regulated during development. Compelling evidence now suggests that dynamic regulation of DNA methylation is mainly achieved through a cyclic enzymatic cascade comprised of cytosine methylation, iterative oxidation of methyl group by TET dioxygenases, and restoration of unmodified cytosines by either replication-dependent dilution or DNA glycosylase-initiated base excision repair. In this review, we discuss the mechanism and function of DNA demethylation in mammalian genomes, focusing particularly on how developmental modulation of the cytosine-modifying pathway is coupled to active reversal of DNA methylation in diverse biological processes.
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Affiliation(s)
- Hao Wu
- Howard Hughes Medical Institute, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA; Harvard Stem Cell Institute, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA; Harvard Stem Cell Institute, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA.
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296
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Tsagaratou A, Rao A. TET proteins and 5-methylcytosine oxidation in the immune system. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2014; 78:1-10. [PMID: 24619230 DOI: 10.1101/sqb.2013.78.020248] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA methylation in the form of 5-methylcytosine (5mC) is essential for normal development in mammals and influences a variety of biological processes, including transcriptional regulation, imprinting, and the maintenance of genomic stability. The recent discovery of TET proteins, which oxidize 5mC to 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine, has changed our understanding of the process of DNA demethylation. Here, we summarize our current knowledge of the roles of DNA methylation and TET proteins in cell differentiation and function. The intensive research on this subject has so far focused primarily on embryonic stem (ES) cells and neurons. In addition, we summarize what is known about DNA methylation in T-cell function.
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Affiliation(s)
- Ageliki Tsagaratou
- La Jolla Institute for Allergy and Immunology, La Jolla, California 92037
| | - Anjana Rao
- La Jolla Institute for Allergy and Immunology, La Jolla, California 92037 Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0636 Sanford Consortium for Regenerative Medicine, La Jolla, California 92037
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297
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Affiliation(s)
- Guanqun Zheng
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago , 929 East 57th Street, Chicago, Illinois 60637, United States
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298
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Abstract
TET-mediated 5-methyl cytosine (5mC) oxidation acts in epigenetic regulation, stem cell development, and cancer. Hu et al. now determine the crystal structure of the TET2 catalytic domain bound to DNA, shedding light on 5mC-DNA substrate recognition and the catalytic mechanism of 5mC oxidation.
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Affiliation(s)
- Chi-Lin Tsai
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - John A Tainer
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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299
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Aik W, Scotti JS, Choi H, Gong L, Demetriades M, Schofield CJ, McDonough MA. Structure of human RNA N⁶-methyladenine demethylase ALKBH5 provides insights into its mechanisms of nucleic acid recognition and demethylation. Nucleic Acids Res 2014; 42:4741-54. [PMID: 24489119 PMCID: PMC3985658 DOI: 10.1093/nar/gku085] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
ALKBH5 is a 2-oxoglutarate (2OG) and ferrous iron-dependent nucleic acid oxygenase (NAOX) that catalyzes the demethylation of N6-methyladenine in RNA. ALKBH5 is upregulated under hypoxia and plays a role in spermatogenesis. We describe a crystal structure of human ALKBH5 (residues 66–292) to 2.0 Å resolution. ALKBH566–292 has a double-stranded β-helix core fold as observed in other 2OG and iron-dependent oxygenase family members. The active site metal is octahedrally coordinated by an HXD…H motif (comprising residues His204, Asp206 and His266) and three water molecules. ALKBH5 shares a nucleotide recognition lid and conserved active site residues with other NAOXs. A large loop (βIV–V) in ALKBH5 occupies a similar region as the L1 loop of the fat mass and obesity-associated protein that is proposed to confer single-stranded RNA selectivity. Unexpectedly, a small molecule inhibitor, IOX3, was observed covalently attached to the side chain of Cys200 located outside of the active site. Modelling substrate into the active site based on other NAOX–nucleic acid complexes reveals conserved residues important for recognition and demethylation mechanisms. The structural insights will aid in the development of inhibitors selective for NAOXs, for use as functional probes and for therapeutic benefit.
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Affiliation(s)
- WeiShen Aik
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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